The state Coastal Commission on Friday rejected the Navy’s sonar program, saying the service must take more care to protect whales and dolphins during training exercises off Southern California.

“I understand you see this 120,000-square mile range as your theater, but the bottom line is we don’t see it that way. That theater is occupied by creatures of the sea,” Commissioner Jana Zimmer said during a meeting in San Diego.

“Because the people of California have worked so hard and so long to create these marine protected areas, you need to start looking at this theater as a theater where some of the seats are reserved.”

The panel’s unanimous vote sets up a possible repeat of a federal lawsuit that ultimately involved the White House and the Supreme Court in 2008.

The Navy is applying for a five-year renewal of its federal marine permit to conduct training over a huge swath of ocean between Hawaii and Southern California. For the California piece, it is required to run the plan past the Coastal Commission.

On Friday, the commissioners said naval officials didn’t supply enough information to support their conclusion that the overall marine mammal count isn’t affected by Navy sonar technology used to locate ships or by detonations at sea.

Afterward, a Navy spokesman said the service will take some time to consider the commission’s decision. Alex Stone, a U.S. Pacific Fleet environmental project manager, said the Navy wants to maintain a good relationship with the state agency.

The Navy doesn’t have to get the commission’s consent to renew its federal permit with the National Marine Fisheries Service or to continue training off California’s coast. But this is where the courts could become involved again.

Michael Jasny of the Natural Resources Defense Council, or NRDC, said if the Navy continues training without the Coastal Commission’s acceptance of the plan, it would “open them up to judicial review.”

In 2007, the NRDC and the Coastal Commission separately sued the Navy over the disputed effects of sonar. In 2008, the Supreme Court sided with the George W. Bush administration in ruling that the White House could exempt Navy sonar training from key environmental laws.

Based on the Navy’s latest training plan, up to 130 marine mammals could be killed and roughly 8.8 million could be harassed by Navy actions during the prescribed five-year period, according to a Coastal Commission staff report.

The NRDC calculates that these figures are 13 times more than anything the Navy has projected before.

Whales and other marine mammals use their own sonar to locate food and mates. That ability can be disrupted — and the mammal’s hearing damaged — by loud noises such as those created by Navy equipment.

The amount of training and testing proposed by the Navy has increased in this application, though officials didn’t provide an aggregate number. Stone said the Navy is considering a larger geographic area for its exercises and included equipment testing in its projections for the first time.

From the Navy’s point of view, the Southern California marine range — 120,000 square miles off the coast California and Mexico — has never been more vital for training. The Pentagon is sending additional forces to the Pacific in response to the growth of China’s military and the aggression of North Korea.

Cmdr. John Doney of the U.S. Third Fleet said sonar is essential for national defense. He pointed to what he described as an emerging threat: the quiet diesel-electric submarine. Of the 500 subs in existence worldwide, 350 are the quiet diesel-electric variety — and the tally is growing.

“They are quieter, they have more endurance. And the diesel-electrics can operate near the coast and in choke points like straits,” Doney said. “Active sonar becomes the most effective tool to locate and track those diesel submarines and the threat they represent.”

He noted that the South Korean warship Cheonan was torpedoed and sunk in 2010 by a North Korean mini-submarine.

“I would submit that the threat is real,” Doney said.

One sticking point for the Coastal Commission on Friday was that the Navy didn’t want to adopt measures suggested by the commission’s staff. The Navy has taken that stance in the past as well.

The commission staff proposed:

•Establishing larger shutdown areas, of up to 2 kilometers, when marine mammals or sea turtles are detected

•Avoiding use of sonar in sensitive areas, including marine sanctuaries and protected areas; zones with blue, fin and gray whales; and shore areas with coastal bottlenose dolphins.

•Improving the training for lookouts, who are tasked with spotting marine mammals during Navy exercises.

•Forming a contingency plan for use of near-shore explosives, if further animal deaths occur.

The last condition refers to the March 2011 incident when at least three long-beaked common dolphins were killed by an explosives drill between a half-mile and 1 mile off the Silver Strand.

Stone, of the U.S. Pacific Fleet, said the Coastal Commission’s conditions aren’t needed because the Navy already uses safeguards such as posting lookouts and using passive sonar to detect large sea creatures.

“These really do work. They are a part of the culture of the Navy. You can go aboard any ship and you will be immediately impressed by how seriously the mitigation measures are taken,” Stone said.

He added that the Navy frowns on the idea of avoiding large sections of water, such as marine sanctuaries, because it cuts down on the realism of training.

As many as 200 people attended the commission hearing, including representatives of Greenpeace, the Sierra Club, the Surfrider Foundation and the Audubon Society.